LAMMPS (24 Aug 2020)
  using 1 OpenMP thread(s) per MPI task
# created by fftool

units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls

special_bonds lj/coul 0.0 0.0 0.5

pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0 coul/tt 4 8.0
pair_modify tail yes
kspace_style pppm 1.0e-5

read_data data.ethylene_glycol
Reading data file ...
  orthogonal box = (0.0000000 0.0000000 0.0000000) to (35.000000 35.000000 35.000000)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  2800 atoms
  scanning bonds ...
  2 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  9 = max dihedrals/atom
  reading bonds ...
  2600 bonds
  reading angles ...
  2800 angles
  reading dihedrals ...
  3000 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0.0      0.0      0.5     
  special bond factors coul:  0.0      0.0      0.5     
     5 = max # of 1-2 neighbors
     6 = max # of 1-3 neighbors
    10 = max # of 1-4 neighbors
    13 = max # of special neighbors
  special bonds CPU = 0.002 seconds
  read_data CPU = 0.023 seconds

pair_coeff    1    1 lj/cut/coul/long     0.057289     3.500000  # CTO CTO ~
pair_coeff    1    2 lj/cut/coul/long     0.091945     3.304542  # CTO OHG ~
pair_coeff    1    3 lj/cut/coul/long     0.038625     2.958040  # CTO H1O ~
pair_coeff    1    4 lj/cut/coul/long     0.000000     0.000000  # CTO HOG ~
pair_coeff    2    2 lj/cut/coul/long     0.147565     3.120000  # OHG OHG ~
pair_coeff    2    3 lj/cut/coul/long     0.061990     2.792848  # OHG H1O ~
pair_coeff    2    4 lj/cut/coul/long     0.000000     0.000000  # OHG HOG ~
pair_coeff    3    3 lj/cut/coul/long     0.026041     2.500000  # H1O H1O ~
pair_coeff    3    4 lj/cut/coul/long     0.000000     0.000000  # H1O HOG ~
pair_coeff    4    4 lj/cut/coul/long     0.000000     0.000000  # HOG HOG ~
pair_coeff    *   5* lj/cut/coul/long     0.000000     0.000000
pair_coeff    1    1 thole   1.662
pair_coeff    1    2 thole   1.561
pair_coeff    1    5 thole   1.662
pair_coeff    1    6 thole   1.561
pair_coeff    2    2 thole   1.467
pair_coeff    2    5 thole   1.561
pair_coeff    2    6 thole   1.467
pair_coeff    5    5 thole   1.662
pair_coeff    5    6 thole   1.561
pair_coeff    6    6 thole   1.467
pair_coeff    2    4 coul/tt  4.5 1.0
pair_coeff    4    6 coul/tt  4.5 1.0
pair_coeff    1    4 coul/tt  4.5 1.0
pair_coeff    4    5 coul/tt  4.5 1.0

group ATOMS type 1 2 3 4
2000 atoms in group ATOMS
group CORES type 1 2
800 atoms in group CORES
group DRUDES type 5 6
800 atoms in group DRUDES

fix DRUDE all drude C C N N D D

fix SHAKE ATOMS shake 0.0001 20 0 b 3 4
     400 = # of size 2 clusters
     400 = # of size 3 clusters
       0 = # of size 4 clusters
       0 = # of frozen angles
  find clusters CPU = 0.001 seconds

neighbor 2.0 bin

timestep 1.0

variable TK equal 298.0
variable TDK equal 1.0
variable PBAR equal 1.0

comm_modify vel yes
velocity ATOMS create ${TK} 12345
velocity ATOMS create 298 12345

compute TATOM ATOMS temp
compute TDRUDE all temp/drude

fix DTDIR all drude/transform/direct
fix TSTAT ATOMS npt temp ${TK} ${TK} 200 iso ${PBAR} ${PBAR} 1000
fix TSTAT ATOMS npt temp 298 ${TK} 200 iso ${PBAR} ${PBAR} 1000
fix TSTAT ATOMS npt temp 298 298 200 iso ${PBAR} ${PBAR} 1000
fix TSTAT ATOMS npt temp 298 298 200 iso 1 ${PBAR} 1000
fix TSTAT ATOMS npt temp 298 298 200 iso 1 1 1000
fix_modify TSTAT temp TATOM press thermo_press
WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1428)
fix TSTDR DRUDES nvt temp ${TDK} ${TDK} 50
fix TSTDR DRUDES nvt temp 1 ${TDK} 50
fix TSTDR DRUDES nvt temp 1 1 50
fix DTINV all drude/transform/inverse

fix ICECUBE all momentum 1000 linear 1 1 1

thermo_style custom step etotal ke pe ebond eangle evdwl ecoul elong   press vol density c_TATOM c_TDRUDE[1] c_TDRUDE[2]
thermo 50

run 500
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
  G vector (1/distance) = 0.41206781
  grid = 54 54 54
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0040479865
  estimated relative force accuracy = 1.2190391e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 250047 157464
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 13
New max number of 1-2 to 1-4 neighbors: 13 (+0)
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10
  ghost atom cutoff = 10
  binsize = 5, bins = 7 7 7
  3 neighbor lists, perpetual/occasional/extra = 3 0 0
  (1) pair lj/cut/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
  (2) pair thole, perpetual, skip from (1)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (3) pair coul/tt, perpetual, skip from (1)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 39.43 | 39.43 | 39.43 Mbytes
Step TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Density c_TATOM c_TDRUDE[1] c_TDRUDE[2] 
       0    2707.9246     1420.362    1287.5627    1474.8647    30.734202   -461.31379    540022.21   -539778.93   -9408.4231        42875   0.48077588          298    294.34401    6.9394757 
      50    1418.4664     1249.502    168.96443    309.99547    480.01554   -495.04808    539716.53   -540017.02    3344.2851    42776.949   0.48187789    252.07241    255.56807    12.841403 
     100     1391.631    1287.2692    104.36186    333.86636    427.43215   -456.38003    539638.17   -540023.61   -3962.1786    42668.283   0.48310512    265.74273    268.23371    3.3477444 
     150    1404.7861    1334.1949    70.591169    285.69315    480.49154   -340.69071    539518.01   -540045.75   -2082.9182    42395.713   0.48621109    274.19438     278.9463    1.6008228 
     200    1425.8199    1378.4982    47.321668    460.35813     459.3409   -415.44782    539411.67    -540044.6    6205.8012    42117.045   0.48942811    284.32248    288.46225    1.1474711 
     250    1451.5312    1408.0791    43.452124    376.36315     598.2256    -302.5574    539235.03    -540053.8   -3523.5224    41843.302   0.49263001    290.29735    294.90585   0.66499891 
     300    1460.3317      1532.45   -72.118296    394.63946    561.19451   -334.56109    539192.83   -540050.12    4984.7253    41569.486   0.49587493    316.03909     320.8862   0.85911251 
     350    1465.3219    1564.1529   -98.830958    418.42916     585.9688   -296.62501    539077.24   -540036.78    740.62275    41386.895   0.49806264    322.55774    327.69261   0.54088355 
     400    1446.0613      1528.77   -82.708678    414.47172    582.41623   -279.89537    539064.81   -540045.35   -1758.0709    41241.935   0.49981326    314.95112    320.11103   0.86624717 
     450    1411.6647    1569.3338   -157.66914    380.54196    668.12309   -290.80881    538968.32   -540032.63    3122.7219    41154.153   0.50087936    323.38401    328.46391    1.1709084 
     500    1366.0173    1653.6398   -287.62246    433.22615    598.36853   -281.95956    538837.44   -540025.77   -2920.9274    41080.823   0.50177344    340.53461    346.03932    1.3737011 
Loop time of 21.2526 on 1 procs for 500 steps with 2800 atoms

Performance: 2.033 ns/day, 11.807 hours/ns, 23.526 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 5.0143     | 5.0143     | 5.0143     |   0.0 | 23.59
Bond    | 0.34285    | 0.34285    | 0.34285    |   0.0 |  1.61
Kspace  | 7.6454     | 7.6454     | 7.6454     |   0.0 | 35.97
Neigh   | 0.36282    | 0.36282    | 0.36282    |   0.0 |  1.71
Comm    | 0.035159   | 0.035159   | 0.035159   |   0.0 |  0.17
Output  | 0.00068069 | 0.00068069 | 0.00068069 |   0.0 |  0.00
Modify  | 7.8451     | 7.8451     | 7.8451     |   0.0 | 36.91
Other   |            | 0.006337   |            |       |  0.03

Nlocal:        2800.00 ave        2800 max        2800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        6816.00 ave        6816 max        6816 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:       446966.0 ave      446966 max      446966 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 446966
Ave neighs/atom = 159.63071
Ave special neighs/atom = 11.714286
Neighbor list builds = 28
Dangerous builds = 0

Total wall time: 0:00:21
